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Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)


  use Bio::Align::ProteinStatistics;
  use Bio::AlignIO;
  my $in = Bio::AlignIO->new(-format => 'fasta',
                            -file   => 'pep-104.fasaln');
  my $aln = $in->next_aln;

  my $pepstats = Bio::Align::ProteinStatistics->new();
  $kimura = $protstats->distance(-align => $aln,
                                 -method => 'Kimura');
  print $kimura->print_matrix;


This object is for generating various statistics from a protein alignment. Mostly it is where pairwise protein distances can be calculated.


D_Kimura - Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, Cambridge.


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AUTHOR - Jason Stajich



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = Bio::Align::ProteinStatistics->new();
 Function: Builds a new Bio::Align::ProteinStatistics object 
 Returns : an instance of Bio::Align::ProteinStatistics
 Args    :


 Title   : distance
 Usage   : my $distance_mat = $stats->distance(-align  => $aln, 
                                               -method => $method);
 Function: Calculates a distance matrix for all pairwise distances of
           sequences in an alignment.
 Returns : L<Bio::Matrix::PhylipDist> object
 Args    : -align  => Bio::Align::AlignI object
           -method => String specifying specific distance method 
                      (implementing class may assume a default)


 Title   : available_distance_methods
 Usage   : my @methods = $stats->available_distance_methods();
 Function: Enumerates the possible distance methods
 Returns : Array of strings
 Args    : none

D - distance methods


 Title   : D_Kimura
 Usage   : my $matrix = $pepstats->D_Kimura($aln);
 Function: Calculate Kimura protein distance (Kimura 1983) which 
           approximates PAM distance
           D = -ln ( 1 - p - 0.2 * p^2 )
 Returns : L<Bio::Matrix::PhylipDist>
 Args    : L<Bio::Align::AlignI>

Data Methods


 Title   : pairwise_stats
 Usage   : $obj->pairwise_stats($newval)
 Returns : value of pairwise_stats
 Args    : newvalue (optional)